Foreign Minister Julie Bishop says Australia will send officials to Indonesia to assist with an investigation into claims asylum seekers were injured under the direction of Australian Navy personnel if it means the allegations will be quickly "scotched".

Footage obtained by the ABC shows several asylum seekers - who Indonesian police say were on a vessel forced back by the Australian Navy on January 6 - being medically assessed for burns on their hands.

Speaking in Washington, Ms Bishop defended the professionalism of Navy personnel but said she cannot imagine for a moment that any of them would have behaved in the way asylum seekers have alleged.

The asylum seekers say they were kicked and burnt when the Australian Navy forced them to touch part of their boat's engine, allegations which police in Indonesia say have been referred to the country's national police headquarters.

"I reject utterly any notion that the Australian Government would condone that sort of behaviour," Ms Bishop told reporters in Washington.

"I cannot imagine for a moment that the professional people that we have in our forces would have behaved in that fashion.

"But of course if there is any cooperation we can extend to ensure that these allegations are scotched then we'd be prepared to do it."

Chief detective Sam Kawengian, in Kupang in Indonesia's east, says so far the only evidence to go by is the burns to the asylum seekers hands, and their statements to police but he is referring the case to the national headquarters.

"From the questioning we did the other day, some said they were tortured... [by] Australian police, or whatever, their authorities," he told the ABC.

"They showed the marks of what they said were inflicted upon them by Australian Navy - but we don't know for sure because the only witnesses are among themselves. That's the information we get from them.

"There were bruises in their arms, legs, some also said that their genitals were hurting - men - they say their genitals were kicked. This is what they said, it's not the result of our investigation."

The claims have surfaced amid increasing tensions between the two countries over the Coalition government's contentious policy of returning vessels which have entered Australian territory without permission.

"I think we still need to clarify these allegations," he told ABC's 7.30 program.

"If it is true, then the government of Australia has clearly violated human rights of the asylum seekers and at the same time they have also violated the territory of Indonesians.

"I think it is a must for the Australian Government to investigate so the authority of Australia don't immediately make a statement to the world that there is no violations of human rights of the asylum seekers that was taking place on the oceans.

Greens want thorough investigation into alleged incident

Yesterday, the Immigration Minister Scott Morrison said people smugglers had a strong motivation for fabricating stories to discredit Australia's border protection policies.

Greens leader Christine Milne says the Government's dismissal of the allegations is not good enough.

"It is just inexcusable to stand there and say 'I have every confidence, therefore I'm not going to look into it'," she said.

"That's what he said about spy agencies as well, and look where we are in the International Court of Justice over East Timor."

Opposition Leader Bill Shorten has backed the professional reputation of Navy personnel, but says their job had been made harder because of the Government's policies.

Mr Shorten says while the reports of mistreatment are concerning, he says it would be better if the Government was open and transparent about what is happening at sea.

"Labor believes that the Navy and its personnel are professional - they have an extremely tough job to do," he told ABC News Breakfast this morning.